Table 1: List of aptamers grouped by organism and type categories, with number of aptamers per category shown in right-most column.
| Organism | Type | Aptamer_Count |
|---|---|---|
| Human | Protein | 7289 |
| Mouse | Protein | 233 |
| Human | Spuriomer | 20 |
| Human | Hybridization Control Elution | 12 |
| Human | Non-Biotin | 10 |
| Human | Non-Cleavable | 4 |
| African clawed frog | Non-Human | 3 |
| Gila monster | Non-Human | 3 |
| Hornet | Non-Human | 3 |
| Jellyfish | Non-Human | 3 |
| Mouse | Non-Human | 3 |
| Thermus thermophilus | Non-Human | 3 |
| Common eastern firefly | Non-Human | 2 |
| European elder | Non-Human | 2 |
| Bacillus stearothermophilus | Non-Human | 1 |
| Ensifer meliloti | Non-Human | 1 |
| HIV-1 | Protein | 1 |
| HIV-2 | Protein | 1 |
| Red alga|Red alga | Non-Human | 1 |
| strain K12 | Non-Human | 1 |
Table 2: Number of human protein aptamers (7289, see Table 1) per quality category. Quality refers to the success with which the human protein-designed aptamer is able to quantify protein intensity in mouse plasma samples.
| Quality | Count |
|---|---|
| High | 2653 |
| Low | 910 |
| Medium | 3726 |
Figure 1: Plots of aptamer counts per sample for A) mouse and B) human datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.
Figure 2: Plots of aptamer counts per sample for A) mouse and B) human pre-normalization datasets above eLoD calculated for each aptamer (eLoD = Median_blank + 4.9MAD_blank). Blue horizontal line indicate the total number of aptamers in the panel (7596). Red horizontal line (mouse only) indicates the number of human protein aptamers assessed to perform with high/medium quality in mouse samples.
Figure 3: Boxplots showing distribution of aptamer intensities by sample for mouse and human datasets, final data and pre-normalization data for each. Plots are color coded by clinical group for both datasets. Most samples in each dataset have similar intensity distributions. Calibrator samples and hemolysis samples (mouse only) show slightly wider distribution ranges. The sole AK mouse sample has a slightly lower-shifted distribution compared to other samples.
Figure 4: Bar graph showing number of aptamers removed by eLoD filter per sample for mouse datasets.
Figure 5: Boxplots showing distribution of removed aptamer counts per sample, grouped by aptamer quality in mouse. Outliers - samples with an irregular number of aptamers removed - are labeled.
Figure 6: Bar graph showing number of aptamers removed by eLoD filter per sample for human datasets.
Figure 7: Bar graph showing distribution of aptamers removed using eLoD filter, categorized by aptamer quality score in mouse system.
Figure 8: Scatter plot showing the intensity distribution for three aptamers: seq.10000.28 (high quality aptamer in mouse), seq.10044.12 (low quality), and seq.10003.15 (medium quality). The low quality aptamer has higher variation then both the medium and high quality aptamers in both the normalized and pre-normalization mouse datasets, although the difference is more apparent in the normalized dataset.
Figure 9: SomaLogic Log2 intensity boxplot distributions
separated by mouse aptamer quality score. All three quality categories
appear to have similar intensity distributions per sample.
Figure 10: Aptamer CV distributions for murine and human data,
grouped and colored by condition. Overall, low CVs are observed in both
species datasets, human having slightly lower aptamer CVs than
murine.
Figure 11: P-value distributions for the wilcox tests performed on the mouse dilution series data (pre-normalization).
Figure 12: Volcano plots showing significantly differentially expressed proteins between mouse dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.
Table 2: Number of aptamers/proteins detected per mouse dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).
| Category | Sample_ID | AptCount |
|---|---|---|
| 35uL | Mouse 35 uL Rep 1 | 7512 |
| 35uL | Mouse 35 uL Rep 2 | 7534 |
| 35uL | Mouse 35 uL Rep 3 | 7540 |
| 55uL | Mouse A Series Rep 1 | 7537 |
| 55uL | Mouse A Series Rep 2 | 7537 |
| 55uL | Mouse A Series Rep 3 | 7550 |
| 55uL Diluted | Mouse B Series Rep 1 | 7491 |
| 55uL Diluted | Mouse B Series Rep 2 | 7403 |
| 55uL Diluted | Mouse B Series Rep 3 | 7421 |
Figure 13: Boxplot FC distributions of murine dilution series
data. Median FC is on target for expected dilutions ratio from 35 to
55µL (0.6x).
Figure 14: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the Hemolysis and Pooled 55uL groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 15: Volcano plots showing significantly differentially expressed proteins between hemolysis and pooled 55uL groups in mouse data, A) normalized, B) pre-normalization.
Figure 16: Hemoglobin intensity results comparing each
hemoglobin-targeting aptamer in the murine suspected hemolysis samples
and murine pooled 55µL samples
| Table_Key | Aptamer_Target | Target_Full_Name |
|---|---|---|
| 1 | seq.17137.160_Beta-globin | Hemoglobin subunit beta |
| 2 | seq.18198.51_HBAT | Hemoglobin subunit theta-1 |
| 3 | seq.19774.8_HBG2 | Hemoglobin subunit gamma-2 |
| 4 | seq.4915.64_Hemoglobin | Hemoglobin |
| 5 | seq.6919.3_HBAZ | Hemoglobin subunit zeta |
| 6 | seq.6992.67_HBD | Hemoglobin subunit delta |
| 7 | seq.7136.107_Hemoglobin epsilon chain | Hemoglobin subunit epsilon |
| 8 | seq.7965.25_HBAT | Hemoglobin subunit theta-1 |
| 9 | seq.9025.5_AHSP | Alpha-hemoglobin-stabilizing protein |
Table 3: Hemoglobin-targeting aptamers with the key used to ID Figure 16 sub-plots with aptamer descriptions.
Reveals differentially abundant proteins in autochthonous PDAC model
Figure 17: P-value distributions for the wilcox tests performed on the mouse data comparing intensity (RFU) values between aptamers in the KMC-PDAC and Healthy Control - Late/KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 18: Volcano plots showing significantly differentially expressed proteins between KMC - PDAC and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in autochthonous lung cancer model
Figure 19: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC-Lung and KP Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 20: Volcano plots showing significantly differentially expressed proteins between KPC-Lung and Healthy Control - Late/KP Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in autochthonous Myc-driven PDAC model
Figure 21: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KMC-PDAC and KMC Control groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 22: Volcano plots showing significantly differentially expressed proteins between KMC-PDAC and KMC Control groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in early lethal PanIN model
Figure 23: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the KPC - Early and Healthy control - early/KP-early groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 24: Volcano plots showing significantly differentially expressed proteins between KPC - early and Healthy control - early/KP - early groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in late lethal PanIN model
Figure 25: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 26: Volcano plots showing significantly differentially expressed proteins between Lethal PanIN - Late/KPC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.
Reveals differentially abundant proteins in non-lethal PanIN model
Figure 27: P-value distributions for the Wilcox tests performed on the mouse data comparing intensity (RFU) values between proteins in the Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups. A) Normalized mouse data, B) Pre-normalization mouse data.
Figure 28: Volcano plots showing significantly differentially expressed proteins between Non-lethal PanIN - Late/KC - Late and Healthy Control - Late/KP-Late groups in mouse data, A) normalized, B) pre-normalization.
Figure 29: P-value distributions for the wilcox tests performed on the human dilution series data (pre-normalization).
Figure 30: Volcano plots showing significantly differentially expressed proteins between human dilution series samples A) 35uL vs. 55uL, B) 35uL vs. 55uL Diluted [35uL sample, 20uL PBS], C) 55uL vs. 55uL Diluted.
Table 4: Number of aptamers/proteins detected per human dilution series sample (pre-normalization). The 55uL Diluted samples have the lowest counts, but all are decently high (max 7596 aptamers).
| Category | Sample_ID | AptCount |
|---|---|---|
| 35uL | Human 35 uL Rep 1 | 7553 |
| 35uL | Human 35 uL Rep 2 | 7558 |
| 35uL | Human 35 uL Rep 3 | 7561 |
| 55uL | Human A Series Rep 1 | 7566 |
| 55uL | Human A Series Rep 2 | 7576 |
| 55uL | Human A Series Rep 3 | 7577 |
| 55uL Diluted | Human B Series Rep 1 | 7503 |
| 55uL Diluted | Human B Series Rep 2 | 7482 |
| 55uL Diluted | Human B Series Rep 3 | 7504 |
Figure 31: Boxplot FC distributions of human dilution series data. Median FC is on target for expected dilutions ratio from 35 to 55µL (0.6x).
Figure 32: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and All Controls groups. A) Normalized human data, B) Pre-normalization human data.
Figure 33: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and All Controls groups in human data, A) normalized, B) pre-normalization.
Figure 34: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign) groups. A) Normalized human data, B) Pre-normalization human data.
Figure 35: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign) groups in human data, A) normalized, B) pre-normalization.
Figure 36: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups. A) Normalized human data, B) Pre-normalization human data.
Figure 37: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Benign Prostatic Hyperplasia) groups in human data, A) normalized, B) pre-normalization.
Figure 38: P-value distributions for the Wilcox tests performed on the human data comparing intensity (RFU) values between proteins in the Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups. A) Normalized human data, B) Pre-normalization human data.
Figure 39: Volcano plots showing significantly differentially expressed proteins between Case (Adenocarcinoma) and Control (Prostatic Intraepithelial Neoplasia) groups in human data, A) normalized, B) pre-normalization.
## [1] "Starting mapping..."
## [1] "Not all UniProts submitted are valid in NCBI (EntrezID) DB. Proceeding with pivot for valid UniProts only."
## [1] "Human uniprots mapped to EntrezID..."
## [1] "Mouse --> Human Entrez ID Orthology Match performed..."
## [1] "All annotation columns successfully added to NCBI-Mapped DF..."
## [1] "UniProt Nomenclature Conversion: Human --> Mouse Complete. KEGG Orthology DB used to address gaps in NCBI DB."
## [1] "Starting mapping..."
## [1] "Not all uniprots submitted are valid in NCBI (EntrezID) DB. Proceeding with pivot for valid uniprots only."
## [1] "Mouse uniprots mapped to EntrezID..."
## [1] "Mouse --> Human Entrez ID Orthology Match performed..."
## [1] "All annotation columns successfully added to NCBI-Mapped DF..."
## [1] "UniProt Nomenclature Conversion: Mouse --> Human Complete. KEGG Orthology DB used to address gaps in NCBI DB."
Figure 40: Figures summarizing the results of cross-platform analysis for the murine KMC-PDAC and KMC control data.
Figure 41: Figures summarizing the results of cross-platform analysis for the human Case v. Control comparison data.
## [1] "Starting mapping..."
## [1] "Not all UniProts submitted are valid in NCBI (EntrezID) DB. Proceeding with pivot for valid UniProts only."
## [1] "Human uniprots mapped to EntrezID..."
## [1] "Mouse --> Human Entrez ID Orthology Match performed..."
## [1] "All annotation columns successfully added to NCBI-Mapped DF..."
## [1] "UniProt Nomenclature Conversion: Human --> Mouse Complete. KEGG Orthology DB used to address gaps in NCBI DB."
## [1] "Starting mapping..."
## [1] "Not all uniprots submitted are valid in NCBI (EntrezID) DB. Proceeding with pivot for valid uniprots only."
## [1] "Mouse uniprots mapped to EntrezID..."
## [1] "Mouse --> Human Entrez ID Orthology Match performed..."
## [1] "All annotation columns successfully added to NCBI-Mapped DF..."
## [1] "UniProt Nomenclature Conversion: Mouse --> Human Complete. KEGG Orthology DB used to address gaps in NCBI DB."
Figure 42: Figures summarizing the results of cross-platform analysis for the murine KMC-PDAC and KMC control Log2 intensity and Log2 ZScore intensity data.
Figure 43: Figures summarizing the results of cross-platform analysis for the human Case v. Control Log2 intensity and Log2 ZScore intensity data.
Figure 44: Histograms showing distribution of SomaLogic and Seer Log2 and Log2 ZScore intensity data for murine KMC-PDAC and KMC control, and human Case and Control.
Table 5: Unique protein counts for each platform (SomaLogic and Seer MS) for the two main studies compared here (murine KMC-PDAC and KMC Control, human Case and Control) and the number of overlapping protein IDs between platforms in each study. For protein groups in Seer IDs, only the first ID is retained to be able to align IDs between Seer and SomaLogic.
| Study | Seer Protein Count Initial | Seer Protein Count 50% Sparsity | Seer Protein Count w/ Alt. Group IDs | SomaLogic Protein Count (pre-eLoD) | SomaLogic Protein Count (post-eLoD) | Overlap Protein Count |
|---|---|---|---|---|---|---|
| Human Prostate Cancer Case v. Control | 1443 | 906 | 906 | 6432 | 6422 | 590 |
| Murine KMC-PDAC v. KMC Control | 7526 | 4085 | 3103 | 6432 | 6412 | 875 |